Can honey bee colony simulation be done in Blender?
I expect you can do a good job of that in blender, within the particle physics settings you can find some boids options, these can be used to simulate a flock of birds so it should do bees just as well. I would have some empties moving from place to place that a swarm would follow to specify the timing of the bees moving.

You can use multiple particle systems so you may want one for the bees hanging around the hive; one (or more) for each group(s) that goes off to the flowers; and one (or more) for each group(s) that returns to the hive.

You can also use particles to place the flowers around the scene.